+Open data
-Basic information
Entry | Database: PDB / ID: 2vj5 | ||||||
---|---|---|---|---|---|---|---|
Title | Shigella flexneri MxiC | ||||||
Components | PROTEIN MXIC | ||||||
Keywords | TRANSPORT PROTEIN / SECRETION REGULATION / T3SS / VIRULENCE / TRANSPORT / TYPE THREE SECRETION SYSTEM | ||||||
Function / homology | Function and homology information protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / host cell / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | SHIGELLA FLEXNERI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structures of the Shigella Flexneri Type 3 Secretion System Protein Mxic Reveal Conformational Variability Amongst Homologues. Authors: Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vj5.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vj5.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vj5_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2vj5_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 2vj5_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 2vj5_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vj5 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vj5 | HTTPS FTP |
-Related structure data
Related structure data | 2vixSC 2vj4C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.818, 0.009, 0.576), Vector: |
-Components
#1: Protein | Mass: 33643.301 Da / Num. of mol.: 2 / Fragment: RESIDUES 74-355 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04640 #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE HSSGLVPRGSH COMES FROM THE EXPRESSION VECTOR. THE NTERMINUS IS ABSENT FROM THE ...THE SEQUENCE HSSGLVPRGS | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.6 % Description: DATA INDEXED WITH LABELIT AND INTEGRATED IN XDS USING THE SUITE OF PROGRAMS XIA2 |
---|---|
Crystal grow | pH: 6.5 Details: 0.2 M NA2SO4, 0.1 M BISTRISPROPANE PH 6.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3→38.6 Å / Num. obs: 18676 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 171 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.5 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VIX Resolution: 3→38.6 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: REFINED IN BUSTER-TNT 2.1.1 WITH RESTRAINTS TO A STRUCTURE REFINED IN REFMAC5
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET SCALING / Bsol: 255 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→38.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|